Hm, it's kind of difficult to choose.
Prototype's bigger, faster, better fighting, better bosses and cool powers. But the gameplay's linear, the story's terrible, AI's an offence and the sidemissions are pretty much just killing things, wich is all the game is about.
Infamous has a great story, interesting characters, a vareity in the gameplay and cool powers.
However it lacks the pase, the size (there's not a scyscraper in the game), bossfights. Also all the powers are different ways of the same weapon.
I have to gowith infamous because I was more entertained by it in the long run. But for the first hours it was clearly prototype